Analyses of the Microbial Diversity across the Human Microbiome

Abstract

Analysis of human body microbial diversity is fundamental to understanding community structure, biology and ecology. The National Institutes of Health Human Microbiome Project (HMP) has provided an unprecedented opportunity to examine microbial diversity within and across body habitats and individuals through pyrosequencing-based profiling of 16 S rRNA gene sequences (16 S) from habits of the oral, skin, distal gut, and vaginal body regions from over 200 healthy individuals enabling the application of statistical techniques. In this study, two approaches were applied to elucidate the nature and extent of human microbiome diversity. First, bootstrap and parametric curve fitting techniques were evaluated to estimate the maximum number of unique taxa, Smax, and taxa discovery rate for habitats across individuals. Next, our results demonstrated that the variation of diversity within low abundant taxa across habitats and individuals was not sufficiently quantified with standard ecological diversity indices. This impact from low abundant taxa motivated us to introduce a novel rank-based diversity measure, the Tail statistic, (“τ”), based on the standard deviation of the rank abundance curve if made symmetric by reflection around the most abundant taxon. Due to τ’s greater sensitivity to low abundant taxa, its application to diversity estimation of taxonomic units using taxonomic dependent and independent methods revealed a greater range of values recovered between individuals versus body habitats, and different patterns of diversity within habitats. The greatest range of τ values within and across individuals was found in stool, which also exhibited the most undiscovered taxa. Oral and skin habitats revealed variable diversity patterns, while vaginal habitats were consistently the least diverse. Collectively, these results demonstrate the importance, and motivate the introduction, of several visualization and analysis methods tuned specifically for next-generation sequence data, further revealing that low abundant taxa serve as an important reservoir of genetic diversity in the human microbiome.

Molecular cartography of the human skin surface in 3D

“…To measure and correlate the region-specific molecular diversity and bacterial diversity, we used the Shannon index (37), a widely used statistical measure of diversity that has previously been used to define high-and low-diversity regions of the skin, and the evenness of the microbial population (5,38,39). We generated topographical maps of both molecular and bacterial diversity, based on Shannon index measurements from n = 394 samples for person 1 and n = 362 samples for person 2.…”

Bacterial bloodstream infections in the allogeneic hematopoietic cell transplant patient: new considerations for a persistent nemesis

“…133 Taxonomic profiling the GI microbiome reveals large diversity in obligate anaerobic bacteria in healthy individuals. 134 The host's immune system keeps the gut microbiota stable and prevents overgrowth of pathogenic species by producing antimicrobial peptides.…”

Intestinal Microbiocenosis, Food Tolerance and Food Allergy. Current State of a Problem

“…в 360 раз больше, чем собственно человеческих [12]. При этом кишечный биоценоз обладает как наибольшим разнооб-разием по числу видов по сравнению с микробиоценоза-ми других экологических ниш, так и наибольшими отли-чиями между разными индивидуумами [12,13].…”

“…Своеобразие рецепторов генетически детерминировано, о чем говорит наличие почти полностью идентичной ана-эробной и аэробной микрофлоры у однояйцевых (в отли-чие от разнояйцевых) близнецов. Тем не менее состав микрофлоры зависит от экологических факторов, вклю-чая питание макроорганизма [10,13,14].…”